snakemake学习（二）

import os
import pandas as pd

# load configfile


# global vals
metadata = pd.read_csv("id", sep="\t").set_index("SampleID", drop=False)

te = pd.read_csv("id.txt", sep="\t").set_index("Te", drop=False)

samples = metadata["SampleID"]
samples_num = len(samples)
te=te["Te"]


    
# includes
def get_fastq(wildcards):
    return metadata.loc[wildcards.samples, ["fq1"]].dropna()

# map trimmed fastq to genome

for i in samples:{
print(i)
}
for id in te:{
print(id)
}
rule all:
    input:
        expand( "fa/{te}/{samples}-{te}.fa",te=te,samples=samples),
#       expand( "out/{te}/{samples}-{te}.bam",te=te,samples=samples),
#        expand( "fa/{te}/{samples}-{te}.fa",te=te,samples=samples)，


rule minimap2:
    input:
        fastq=("raw_data/{samples}.fq.gz"),
    
    output:
#        bam = ("out/{te}/{samples}-{te}.bam"),
        fa = ("fa/{te}/{samples}-{te}.fa"),

#       fa = ("fa/{te}/{samples}-{te}.fa"),

    shell:
        """minimap2 -ax map-pb  mini/{wildcards.te}.fa {input} |awk -F "\\t" '{{if ( ($1!~/^@/) && (($2==16) ) ) {{print ">"$1"\\n"$10}}}}' > {output.fa} """

##注意shell脚本
#        """minimap2 -ax map-pb  mini/{wildcards.te}.fa {input} | samtools view -bS -@ 22 - > {output.bam} && samtools view {output.bam} | awk -F "\t" '{if ( ($1!~/^@/) && (($2==16) ) ) {print ">"$1"\n"$10}}' > {output.fa} """


#rule bam2fq:
#    input:
#        bam = ("out/{wildcards.te}/{wildcards.samples}-{wildcards.te}.bam"),
#    output:
#        fa = ("fa/{wildcards.te}/{wildcards.samples}-{wildcards.te}.fa"),
#    shell:
#        """samtools view {input} | awk -F "\t" '{if ( ($1!~/^@/) && (($2==16) ) ) {print ">"$1"\n"$10}}' > {output}"""